Starting phenix.real_space_refine on Thu Mar 5 23:00:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v79_31763/03_2026/7v79_31763.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v79_31763/03_2026/7v79_31763.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v79_31763/03_2026/7v79_31763.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v79_31763/03_2026/7v79_31763.map" model { file = "/net/cci-nas-00/data/ceres_data/7v79_31763/03_2026/7v79_31763.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v79_31763/03_2026/7v79_31763.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.067 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 16341 2.51 5 N 4135 2.21 5 O 5090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25677 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 8110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8110 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 52, 'TRANS': 985} Chain breaks: 7 Chain: "B" Number of atoms: 8166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 8166 Classifications: {'peptide': 1044} Link IDs: {'PTRANS': 53, 'TRANS': 990} Chain breaks: 7 Chain: "C" Number of atoms: 8158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1043, 8158 Classifications: {'peptide': 1043} Link IDs: {'PTRANS': 53, 'TRANS': 989} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 6.10, per 1000 atoms: 0.24 Number of scatterers: 25677 At special positions: 0 Unit cell: (144.1, 147.4, 196.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 5090 8.00 N 4135 7.00 C 16341 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 122 " " NAG A2003 " - " ASN A 603 " " NAG A2004 " - " ASN A 657 " " NAG A2005 " - " ASN A 20 " " NAG A2006 " - " ASN A 188 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 122 " " NAG B2003 " - " ASN B 234 " " NAG B2004 " - " ASN B 331 " " NAG B2005 " - " ASN B 603 " " NAG B2006 " - " ASN B 657 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 122 " " NAG C2003 " - " ASN C 331 " " NAG C2004 " - " ASN C 603 " " NAG C2005 " - " ASN C 657 " " NAG C2007 " - " ASN C 188 " " NAG D 1 " - " ASN A 165 " " NAG F 1 " - " ASN A 282 " " NAG G 1 " - " ASN A 331 " " NAG H 1 " - " ASN A 343 " " NAG I 1 " - " ASN A 616 " " NAG J 1 " - " ASN A 709 " " NAG K 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1074 " " NAG N 1 " - " ASN A1098 " " NAG O 1 " - " ASN A1134 " " NAG P 1 " - " ASN B 165 " " NAG Q 1 " - " ASN B 282 " " NAG R 1 " - " ASN B 343 " " NAG S 1 " - " ASN B 616 " " NAG T 1 " - " ASN B 709 " " NAG U 1 " - " ASN B 717 " " NAG V 1 " - " ASN B 801 " " NAG W 1 " - " ASN B1074 " " NAG X 1 " - " ASN B1098 " " NAG Y 1 " - " ASN B1134 " " NAG Z 1 " - " ASN B 20 " " NAG a 1 " - " ASN C 165 " " NAG c 1 " - " ASN C 282 " " NAG d 1 " - " ASN C 343 " " NAG e 1 " - " ASN C 616 " " NAG f 1 " - " ASN C 709 " " NAG g 1 " - " ASN C 717 " " NAG h 1 " - " ASN C 801 " " NAG i 1 " - " ASN C1074 " " NAG j 1 " - " ASN C1098 " " NAG k 1 " - " ASN C1134 " Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 1.0 seconds 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5848 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 47 sheets defined 25.0% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.430A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.831A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.324A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.575A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 898 through 910 removed outlier: 4.203A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.623A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.800A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.857A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.565A pdb=" N GLU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.436A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.172A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.553A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.695A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 633 through 638 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.976A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.721A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.675A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 898 through 908 removed outlier: 3.607A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.664A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.660A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.615A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.099A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.778A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.500A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.671A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.619A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.907A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.567A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 638 removed outlier: 4.025A pdb=" N THR C 638 " --> pdb=" O VAL C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.550A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.546A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.850A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.781A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.828A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.605A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.028A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.088A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.575A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.360A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.613A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASN C 540 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.148A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.651A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.841A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.755A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.165A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 573 through 576 removed outlier: 3.932A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.097A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 712 Processing sheet with id=AB5, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.610A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.572A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.759A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.852A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.575A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.065A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.572A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.585A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 326 through 328 removed outlier: 5.700A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.313A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.271A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD3, first strand: chain 'B' and resid 717 through 719 Processing sheet with id=AD4, first strand: chain 'B' and resid 722 through 728 removed outlier: 3.530A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.544A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.038A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.465A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.970A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.999A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.537A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.595A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.512A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.744A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.565A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.565A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.547A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1122 988 hydrogen bonds defined for protein. 2685 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.53 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8030 1.34 - 1.46: 6653 1.46 - 1.58: 11426 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 26247 Sorted by residual: bond pdb=" C1 NAG W 1 " pdb=" O5 NAG W 1 " ideal model delta sigma weight residual 1.406 1.469 -0.063 2.00e-02 2.50e+03 9.91e+00 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.44e+00 bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.43e+00 bond pdb=" C1 NAG b 2 " pdb=" O5 NAG b 2 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.48e+00 bond pdb=" C1 NAG C2003 " pdb=" O5 NAG C2003 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.72e+00 ... (remaining 26242 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 34476 1.60 - 3.21: 1114 3.21 - 4.81: 103 4.81 - 6.42: 23 6.42 - 8.02: 8 Bond angle restraints: 35724 Sorted by residual: angle pdb=" N GLY B 103 " pdb=" CA GLY B 103 " pdb=" C GLY B 103 " ideal model delta sigma weight residual 111.42 117.57 -6.15 1.42e+00 4.96e-01 1.88e+01 angle pdb=" N CYS A 525 " pdb=" CA CYS A 525 " pdb=" C CYS A 525 " ideal model delta sigma weight residual 108.14 113.62 -5.48 1.52e+00 4.33e-01 1.30e+01 angle pdb=" N GLY C 103 " pdb=" CA GLY C 103 " pdb=" C GLY C 103 " ideal model delta sigma weight residual 112.06 117.74 -5.68 1.66e+00 3.63e-01 1.17e+01 angle pdb=" C ASN C1074 " pdb=" N PHE C1075 " pdb=" CA PHE C1075 " ideal model delta sigma weight residual 122.36 127.38 -5.02 1.60e+00 3.91e-01 9.86e+00 angle pdb=" C ARG C 102 " pdb=" N GLY C 103 " pdb=" CA GLY C 103 " ideal model delta sigma weight residual 122.67 119.46 3.21 1.10e+00 8.26e-01 8.51e+00 ... (remaining 35719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.01: 15580 23.01 - 46.02: 910 46.02 - 69.04: 145 69.04 - 92.05: 41 92.05 - 115.06: 67 Dihedral angle restraints: 16743 sinusoidal: 7644 harmonic: 9099 Sorted by residual: dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual 93.00 173.73 -80.73 1 1.00e+01 1.00e-02 8.05e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual -86.00 -6.95 -79.05 1 1.00e+01 1.00e-02 7.78e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -7.79 -78.21 1 1.00e+01 1.00e-02 7.64e+01 ... (remaining 16740 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 4242 0.122 - 0.243: 53 0.243 - 0.365: 6 0.365 - 0.486: 2 0.486 - 0.608: 1 Chirality restraints: 4304 Sorted by residual: chirality pdb=" C1 NAG f 1 " pdb=" ND2 ASN C 709 " pdb=" C2 NAG f 1 " pdb=" O5 NAG f 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.23e+00 chirality pdb=" C1 NAG i 1 " pdb=" ND2 ASN C1074 " pdb=" C2 NAG i 1 " pdb=" O5 NAG i 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.78e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.40e+00 ... (remaining 4301 not shown) Planarity restraints: 4542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 81 " 0.057 5.00e-02 4.00e+02 8.70e-02 1.21e+01 pdb=" N PRO A 82 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " -0.037 5.00e-02 4.00e+02 5.64e-02 5.09e+00 pdb=" N PRO A 987 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 906 " -0.018 2.00e-02 2.50e+03 1.70e-02 5.06e+00 pdb=" CG PHE B 906 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE B 906 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE B 906 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 906 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 906 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 906 " -0.001 2.00e-02 2.50e+03 ... (remaining 4539 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 406 2.66 - 3.22: 23896 3.22 - 3.78: 36977 3.78 - 4.34: 49031 4.34 - 4.90: 83072 Nonbonded interactions: 193382 Sorted by model distance: nonbonded pdb=" OD1 ASN A 125 " pdb=" O3 NAG A2002 " model vdw 2.099 3.040 nonbonded pdb=" OG1 THR B 323 " pdb=" OE1 GLU B 324 " model vdw 2.125 3.040 nonbonded pdb=" OG SER A 349 " pdb=" O LEU A 452 " model vdw 2.151 3.040 nonbonded pdb=" O GLU A 661 " pdb=" OH TYR A 695 " model vdw 2.169 3.040 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.175 3.040 ... (remaining 193377 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 621 or resid 635 through 827 or resid 855 throu \ gh 2006)) selection = (chain 'C' and (resid 14 through 621 or resid 635 through 827 or resid 855 throu \ gh 2006)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.310 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 26372 Z= 0.255 Angle : 0.702 19.862 36059 Z= 0.339 Chirality : 0.050 0.608 4304 Planarity : 0.004 0.087 4492 Dihedral : 16.277 115.059 10775 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.85 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.15), residues: 3077 helix: 1.39 (0.21), residues: 680 sheet: 0.26 (0.19), residues: 756 loop : -1.41 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1039 TYR 0.023 0.001 TYR A 873 PHE 0.039 0.002 PHE B 906 TRP 0.017 0.001 TRP B 886 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00563 (26247) covalent geometry : angle 0.65580 (35724) SS BOND : bond 0.00374 ( 40) SS BOND : angle 1.75935 ( 80) hydrogen bonds : bond 0.13078 ( 972) hydrogen bonds : angle 6.05231 ( 2685) link_BETA1-4 : bond 0.00405 ( 35) link_BETA1-4 : angle 1.87338 ( 105) link_NAG-ASN : bond 0.00555 ( 50) link_NAG-ASN : angle 3.45019 ( 150) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4929 (pmm) cc_final: 0.3533 (tmm) REVERT: A 187 LYS cc_start: 0.7014 (mmmm) cc_final: 0.6801 (tptp) REVERT: A 210 ILE cc_start: 0.8373 (tp) cc_final: 0.8085 (tp) REVERT: A 224 GLU cc_start: 0.7489 (pp20) cc_final: 0.6894 (pp20) REVERT: A 241 LEU cc_start: 0.6761 (mt) cc_final: 0.6513 (mt) REVERT: A 309 GLU cc_start: 0.7613 (mp0) cc_final: 0.7331 (pm20) REVERT: A 529 LYS cc_start: 0.8435 (mmpt) cc_final: 0.8122 (mmmt) REVERT: A 663 ASP cc_start: 0.8346 (m-30) cc_final: 0.8125 (m-30) REVERT: A 675 GLN cc_start: 0.5109 (pp30) cc_final: 0.4884 (tm-30) REVERT: A 950 ASP cc_start: 0.7768 (m-30) cc_final: 0.7218 (m-30) REVERT: A 1092 GLU cc_start: 0.7659 (tp30) cc_final: 0.7454 (pt0) REVERT: B 41 LYS cc_start: 0.7728 (mttt) cc_final: 0.7430 (mttm) REVERT: B 101 ILE cc_start: 0.7432 (mm) cc_final: 0.7184 (mp) REVERT: B 314 GLN cc_start: 0.8702 (tt0) cc_final: 0.8222 (mt0) REVERT: B 461 LEU cc_start: 0.8118 (mt) cc_final: 0.7876 (mt) REVERT: B 950 ASP cc_start: 0.7757 (m-30) cc_final: 0.7386 (m-30) REVERT: B 969 ASN cc_start: 0.8003 (t0) cc_final: 0.7798 (t0) REVERT: B 988 GLU cc_start: 0.7284 (pm20) cc_final: 0.6961 (pm20) REVERT: B 1114 ILE cc_start: 0.8737 (mt) cc_final: 0.8482 (tt) REVERT: C 429 PHE cc_start: 0.8192 (t80) cc_final: 0.7822 (t80) REVERT: C 564 GLN cc_start: 0.7268 (mm110) cc_final: 0.6848 (mm-40) REVERT: C 581 THR cc_start: 0.7969 (m) cc_final: 0.6821 (m) REVERT: C 740 MET cc_start: 0.7742 (tpt) cc_final: 0.7356 (mtt) REVERT: C 1002 GLN cc_start: 0.7610 (tp-100) cc_final: 0.7366 (mt0) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.1545 time to fit residues: 58.5993 Evaluate side-chains 173 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 0.0050 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 2.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN C 239 GLN C 394 ASN C 856 ASN C 901 GLN C1106 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.193892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.146485 restraints weight = 33384.676| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 3.61 r_work: 0.3558 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 26372 Z= 0.184 Angle : 0.681 19.995 36059 Z= 0.325 Chirality : 0.049 0.420 4304 Planarity : 0.004 0.064 4492 Dihedral : 12.553 102.996 5222 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.97 % Favored : 95.00 % Rotamer: Outliers : 0.81 % Allowed : 7.11 % Favored : 92.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.15), residues: 3077 helix: 1.33 (0.21), residues: 677 sheet: 0.25 (0.19), residues: 745 loop : -1.42 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1039 TYR 0.025 0.001 TYR C 453 PHE 0.030 0.002 PHE B 906 TRP 0.010 0.001 TRP C 104 HIS 0.005 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00452 (26247) covalent geometry : angle 0.63887 (35724) SS BOND : bond 0.00415 ( 40) SS BOND : angle 1.64761 ( 80) hydrogen bonds : bond 0.05919 ( 972) hydrogen bonds : angle 5.12686 ( 2685) link_BETA1-4 : bond 0.00596 ( 35) link_BETA1-4 : angle 1.79864 ( 105) link_NAG-ASN : bond 0.00530 ( 50) link_NAG-ASN : angle 3.23484 ( 150) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4933 (pmm) cc_final: 0.3615 (tmm) REVERT: A 187 LYS cc_start: 0.7293 (mmmm) cc_final: 0.7079 (tptp) REVERT: A 210 ILE cc_start: 0.8546 (tp) cc_final: 0.8284 (tp) REVERT: A 529 LYS cc_start: 0.8550 (mmpt) cc_final: 0.8344 (mmmt) REVERT: A 663 ASP cc_start: 0.8467 (m-30) cc_final: 0.8162 (m-30) REVERT: A 675 GLN cc_start: 0.5551 (pp30) cc_final: 0.5346 (tm-30) REVERT: A 754 LEU cc_start: 0.8314 (pp) cc_final: 0.7948 (mt) REVERT: A 878 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7675 (tt) REVERT: A 950 ASP cc_start: 0.8194 (m-30) cc_final: 0.7927 (m-30) REVERT: A 1132 ILE cc_start: 0.8658 (pt) cc_final: 0.8449 (pt) REVERT: B 41 LYS cc_start: 0.8197 (mttt) cc_final: 0.7956 (mttm) REVERT: B 101 ILE cc_start: 0.8011 (mm) cc_final: 0.7690 (mp) REVERT: B 351 TYR cc_start: 0.7501 (p90) cc_final: 0.6777 (p90) REVERT: B 950 ASP cc_start: 0.8275 (m-30) cc_final: 0.8073 (m-30) REVERT: C 508 TYR cc_start: 0.7567 (m-80) cc_final: 0.7246 (m-80) REVERT: C 564 GLN cc_start: 0.7599 (mm110) cc_final: 0.7327 (mm-40) REVERT: C 581 THR cc_start: 0.8310 (m) cc_final: 0.7918 (p) REVERT: C 740 MET cc_start: 0.8185 (tpt) cc_final: 0.7817 (mtt) REVERT: C 814 LYS cc_start: 0.9002 (mmtt) cc_final: 0.8659 (mmmt) REVERT: C 950 ASP cc_start: 0.8318 (t70) cc_final: 0.7901 (m-30) outliers start: 22 outliers final: 16 residues processed: 192 average time/residue: 0.1585 time to fit residues: 49.8156 Evaluate side-chains 178 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 934 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 84 optimal weight: 3.9990 chunk 296 optimal weight: 0.5980 chunk 298 optimal weight: 0.5980 chunk 286 optimal weight: 0.5980 chunk 87 optimal weight: 20.0000 chunk 306 optimal weight: 0.7980 chunk 260 optimal weight: 1.9990 chunk 250 optimal weight: 0.5980 chunk 293 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.195596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.149194 restraints weight = 33416.951| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 3.80 r_work: 0.3576 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26372 Z= 0.117 Angle : 0.617 19.717 36059 Z= 0.290 Chirality : 0.046 0.377 4304 Planarity : 0.004 0.056 4492 Dihedral : 10.669 97.003 5222 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.42 % Favored : 95.55 % Rotamer: Outliers : 1.17 % Allowed : 9.34 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.15), residues: 3077 helix: 1.60 (0.21), residues: 667 sheet: 0.42 (0.19), residues: 722 loop : -1.35 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 214 TYR 0.022 0.001 TYR C 453 PHE 0.019 0.001 PHE B 238 TRP 0.010 0.001 TRP B 353 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00262 (26247) covalent geometry : angle 0.57029 (35724) SS BOND : bond 0.00384 ( 40) SS BOND : angle 1.31356 ( 80) hydrogen bonds : bond 0.04987 ( 972) hydrogen bonds : angle 4.83787 ( 2685) link_BETA1-4 : bond 0.00496 ( 35) link_BETA1-4 : angle 1.87223 ( 105) link_NAG-ASN : bond 0.00548 ( 50) link_NAG-ASN : angle 3.29049 ( 150) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4959 (pmm) cc_final: 0.3731 (tmm) REVERT: A 187 LYS cc_start: 0.7294 (mmmm) cc_final: 0.7069 (tptp) REVERT: A 210 ILE cc_start: 0.8583 (tp) cc_final: 0.8374 (tp) REVERT: A 334 ASN cc_start: 0.9196 (t0) cc_final: 0.8561 (t0) REVERT: A 529 LYS cc_start: 0.8531 (mmpt) cc_final: 0.8308 (mmmt) REVERT: A 663 ASP cc_start: 0.8419 (m-30) cc_final: 0.8154 (m-30) REVERT: A 754 LEU cc_start: 0.8268 (pp) cc_final: 0.8042 (mt) REVERT: A 1132 ILE cc_start: 0.8590 (pt) cc_final: 0.8341 (pt) REVERT: B 101 ILE cc_start: 0.8008 (mm) cc_final: 0.7662 (mp) REVERT: B 168 PHE cc_start: 0.8050 (t80) cc_final: 0.7638 (t80) REVERT: B 175 PHE cc_start: 0.8090 (m-10) cc_final: 0.7778 (m-10) REVERT: B 351 TYR cc_start: 0.7563 (p90) cc_final: 0.6917 (p90) REVERT: C 168 PHE cc_start: 0.8085 (t80) cc_final: 0.7813 (t80) REVERT: C 551 VAL cc_start: 0.8073 (OUTLIER) cc_final: 0.7826 (m) REVERT: C 564 GLN cc_start: 0.7578 (mm110) cc_final: 0.7299 (mm-40) REVERT: C 740 MET cc_start: 0.8144 (tpt) cc_final: 0.7817 (mtt) REVERT: C 814 LYS cc_start: 0.8978 (mmtt) cc_final: 0.8651 (mmmt) REVERT: C 918 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8533 (mm-30) REVERT: C 950 ASP cc_start: 0.8288 (t70) cc_final: 0.7904 (m-30) outliers start: 32 outliers final: 20 residues processed: 204 average time/residue: 0.1429 time to fit residues: 48.7770 Evaluate side-chains 187 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 114 optimal weight: 9.9990 chunk 250 optimal weight: 5.9990 chunk 256 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 chunk 252 optimal weight: 10.0000 chunk 16 optimal weight: 0.4980 chunk 43 optimal weight: 30.0000 chunk 5 optimal weight: 0.9980 chunk 182 optimal weight: 0.9980 chunk 29 optimal weight: 20.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.193830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.147837 restraints weight = 33106.545| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 3.76 r_work: 0.3537 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 26372 Z= 0.156 Angle : 0.633 19.659 36059 Z= 0.301 Chirality : 0.048 0.394 4304 Planarity : 0.004 0.054 4492 Dihedral : 9.761 92.368 5222 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.84 % Favored : 95.13 % Rotamer: Outliers : 1.91 % Allowed : 10.99 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.15), residues: 3077 helix: 1.53 (0.21), residues: 667 sheet: 0.41 (0.19), residues: 721 loop : -1.36 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1039 TYR 0.029 0.001 TYR C 453 PHE 0.022 0.002 PHE A1121 TRP 0.008 0.001 TRP B 436 HIS 0.004 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00379 (26247) covalent geometry : angle 0.58740 (35724) SS BOND : bond 0.00343 ( 40) SS BOND : angle 1.70698 ( 80) hydrogen bonds : bond 0.05389 ( 972) hydrogen bonds : angle 4.79094 ( 2685) link_BETA1-4 : bond 0.00489 ( 35) link_BETA1-4 : angle 1.89570 ( 105) link_NAG-ASN : bond 0.00499 ( 50) link_NAG-ASN : angle 3.17761 ( 150) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 173 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.6573 (p90) cc_final: 0.5962 (p90) REVERT: A 153 MET cc_start: 0.4869 (pmm) cc_final: 0.3666 (tmm) REVERT: A 187 LYS cc_start: 0.7365 (mmmm) cc_final: 0.7133 (tptp) REVERT: A 210 ILE cc_start: 0.8671 (tp) cc_final: 0.8459 (tp) REVERT: A 212 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6871 (tt) REVERT: A 234 ASN cc_start: 0.6358 (t0) cc_final: 0.6090 (t0) REVERT: A 334 ASN cc_start: 0.9189 (t0) cc_final: 0.8558 (t0) REVERT: A 529 LYS cc_start: 0.8530 (mmpt) cc_final: 0.8311 (mmmt) REVERT: A 663 ASP cc_start: 0.8405 (m-30) cc_final: 0.8132 (m-30) REVERT: A 754 LEU cc_start: 0.8299 (pp) cc_final: 0.7942 (mt) REVERT: A 878 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7580 (tt) REVERT: A 996 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8563 (mp) REVERT: A 1132 ILE cc_start: 0.8851 (pt) cc_final: 0.8595 (pt) REVERT: B 101 ILE cc_start: 0.8027 (mm) cc_final: 0.7662 (mp) REVERT: B 351 TYR cc_start: 0.7537 (p90) cc_final: 0.6903 (p90) REVERT: B 988 GLU cc_start: 0.7786 (pm20) cc_final: 0.7333 (pm20) REVERT: C 168 PHE cc_start: 0.8239 (t80) cc_final: 0.8020 (t80) REVERT: C 347 PHE cc_start: 0.8128 (m-10) cc_final: 0.7880 (m-10) REVERT: C 551 VAL cc_start: 0.8064 (OUTLIER) cc_final: 0.7821 (m) REVERT: C 564 GLN cc_start: 0.7645 (mm110) cc_final: 0.7342 (mm-40) REVERT: C 740 MET cc_start: 0.8359 (tpt) cc_final: 0.7983 (mtt) REVERT: C 814 LYS cc_start: 0.8974 (mmtt) cc_final: 0.8658 (mmmt) REVERT: C 918 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: C 950 ASP cc_start: 0.8310 (t70) cc_final: 0.7950 (m-30) outliers start: 52 outliers final: 33 residues processed: 210 average time/residue: 0.1391 time to fit residues: 49.7298 Evaluate side-chains 205 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 65 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 210 optimal weight: 0.7980 chunk 127 optimal weight: 0.0770 chunk 1 optimal weight: 2.9990 chunk 229 optimal weight: 0.8980 chunk 303 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 115 optimal weight: 6.9990 chunk 308 optimal weight: 1.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.195619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.148880 restraints weight = 32916.643| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 3.34 r_work: 0.3600 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26372 Z= 0.116 Angle : 0.595 19.532 36059 Z= 0.279 Chirality : 0.046 0.370 4304 Planarity : 0.004 0.052 4492 Dihedral : 9.048 86.021 5222 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.19 % Favored : 95.78 % Rotamer: Outliers : 2.02 % Allowed : 11.95 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.15), residues: 3077 helix: 1.74 (0.21), residues: 655 sheet: 0.46 (0.19), residues: 728 loop : -1.31 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 237 TYR 0.023 0.001 TYR C 453 PHE 0.017 0.001 PHE C 456 TRP 0.008 0.001 TRP A 886 HIS 0.002 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00267 (26247) covalent geometry : angle 0.55116 (35724) SS BOND : bond 0.00292 ( 40) SS BOND : angle 1.38309 ( 80) hydrogen bonds : bond 0.04696 ( 972) hydrogen bonds : angle 4.64118 ( 2685) link_BETA1-4 : bond 0.00527 ( 35) link_BETA1-4 : angle 1.97739 ( 105) link_NAG-ASN : bond 0.00525 ( 50) link_NAG-ASN : angle 3.02296 ( 150) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 167 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4715 (pmm) cc_final: 0.3598 (tmm) REVERT: A 187 LYS cc_start: 0.7414 (mmmm) cc_final: 0.7175 (tptp) REVERT: A 210 ILE cc_start: 0.8683 (tp) cc_final: 0.8481 (tp) REVERT: A 212 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.6790 (tt) REVERT: A 234 ASN cc_start: 0.6429 (t0) cc_final: 0.6161 (t0) REVERT: A 334 ASN cc_start: 0.9192 (t0) cc_final: 0.8573 (t0) REVERT: A 563 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.6288 (mp10) REVERT: A 663 ASP cc_start: 0.8347 (m-30) cc_final: 0.8119 (m-30) REVERT: A 754 LEU cc_start: 0.8268 (pp) cc_final: 0.8051 (mt) REVERT: A 878 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7717 (tt) REVERT: A 984 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8206 (pp) REVERT: A 1132 ILE cc_start: 0.8789 (pt) cc_final: 0.8513 (pt) REVERT: B 101 ILE cc_start: 0.8023 (mm) cc_final: 0.7662 (mp) REVERT: B 351 TYR cc_start: 0.7585 (p90) cc_final: 0.6941 (p90) REVERT: B 569 ILE cc_start: 0.4424 (OUTLIER) cc_final: 0.4170 (mp) REVERT: C 32 PHE cc_start: 0.7868 (m-10) cc_final: 0.7464 (m-80) REVERT: C 168 PHE cc_start: 0.8176 (t80) cc_final: 0.7961 (t80) REVERT: C 347 PHE cc_start: 0.8117 (m-10) cc_final: 0.7824 (m-10) REVERT: C 414 GLN cc_start: 0.7915 (mm-40) cc_final: 0.7476 (mt0) REVERT: C 551 VAL cc_start: 0.8016 (OUTLIER) cc_final: 0.7801 (m) REVERT: C 564 GLN cc_start: 0.7615 (mm110) cc_final: 0.7334 (mm-40) REVERT: C 740 MET cc_start: 0.8314 (tpt) cc_final: 0.7974 (mtt) REVERT: C 814 LYS cc_start: 0.8954 (mmtt) cc_final: 0.8651 (mmmt) REVERT: C 918 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.7455 (mp0) REVERT: C 950 ASP cc_start: 0.8243 (t70) cc_final: 0.7919 (m-30) outliers start: 55 outliers final: 31 residues processed: 208 average time/residue: 0.1501 time to fit residues: 52.4190 Evaluate side-chains 197 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 254 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 245 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 286 optimal weight: 0.9980 chunk 115 optimal weight: 10.0000 chunk 196 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 chunk 252 optimal weight: 0.8980 chunk 307 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.194741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.148260 restraints weight = 33166.596| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 3.64 r_work: 0.3559 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26372 Z= 0.134 Angle : 0.612 19.592 36059 Z= 0.287 Chirality : 0.046 0.388 4304 Planarity : 0.004 0.053 4492 Dihedral : 8.588 78.714 5222 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.24 % Allowed : 12.61 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.15), residues: 3077 helix: 1.70 (0.21), residues: 655 sheet: 0.43 (0.19), residues: 729 loop : -1.32 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 357 TYR 0.028 0.001 TYR C 453 PHE 0.020 0.001 PHE A1121 TRP 0.007 0.001 TRP A 886 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00319 (26247) covalent geometry : angle 0.56902 (35724) SS BOND : bond 0.00311 ( 40) SS BOND : angle 1.40295 ( 80) hydrogen bonds : bond 0.04931 ( 972) hydrogen bonds : angle 4.64590 ( 2685) link_BETA1-4 : bond 0.00550 ( 35) link_BETA1-4 : angle 1.98277 ( 105) link_NAG-ASN : bond 0.00489 ( 50) link_NAG-ASN : angle 3.02678 ( 150) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 167 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.6559 (p90) cc_final: 0.5993 (p90) REVERT: A 153 MET cc_start: 0.4643 (pmm) cc_final: 0.3548 (tmm) REVERT: A 187 LYS cc_start: 0.7409 (mmmm) cc_final: 0.7165 (tptp) REVERT: A 212 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6851 (tt) REVERT: A 334 ASN cc_start: 0.9174 (t0) cc_final: 0.8555 (t0) REVERT: A 563 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.6305 (mp10) REVERT: A 663 ASP cc_start: 0.8357 (m-30) cc_final: 0.8118 (m-30) REVERT: A 754 LEU cc_start: 0.8295 (pp) cc_final: 0.8052 (mt) REVERT: A 878 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7622 (tt) REVERT: A 984 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8109 (pp) REVERT: A 996 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8494 (mp) REVERT: A 1132 ILE cc_start: 0.8881 (pt) cc_final: 0.8624 (pt) REVERT: B 101 ILE cc_start: 0.8091 (mm) cc_final: 0.7737 (mp) REVERT: B 351 TYR cc_start: 0.7567 (p90) cc_final: 0.6944 (p90) REVERT: B 396 TYR cc_start: 0.7623 (m-80) cc_final: 0.7407 (m-10) REVERT: B 988 GLU cc_start: 0.7776 (pm20) cc_final: 0.7574 (pm20) REVERT: C 32 PHE cc_start: 0.7902 (m-10) cc_final: 0.7487 (m-80) REVERT: C 168 PHE cc_start: 0.8191 (t80) cc_final: 0.7988 (t80) REVERT: C 347 PHE cc_start: 0.8098 (m-10) cc_final: 0.7751 (m-10) REVERT: C 414 GLN cc_start: 0.7948 (mm-40) cc_final: 0.7510 (mt0) REVERT: C 551 VAL cc_start: 0.7981 (OUTLIER) cc_final: 0.7775 (m) REVERT: C 564 GLN cc_start: 0.7601 (mm110) cc_final: 0.7319 (mm-40) REVERT: C 569 ILE cc_start: 0.5797 (OUTLIER) cc_final: 0.5424 (mp) REVERT: C 740 MET cc_start: 0.8501 (tpt) cc_final: 0.7997 (mtt) REVERT: C 814 LYS cc_start: 0.8962 (mmtt) cc_final: 0.8658 (mmmt) REVERT: C 918 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.7448 (mp0) REVERT: C 950 ASP cc_start: 0.8282 (t70) cc_final: 0.7950 (m-30) outliers start: 61 outliers final: 40 residues processed: 216 average time/residue: 0.1490 time to fit residues: 54.4911 Evaluate side-chains 209 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 161 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 116 optimal weight: 3.9990 chunk 227 optimal weight: 20.0000 chunk 184 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 152 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 197 optimal weight: 0.9990 chunk 155 optimal weight: 0.3980 chunk 41 optimal weight: 0.8980 chunk 150 optimal weight: 0.0370 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN B 115 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.195817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.148740 restraints weight = 32993.151| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 3.69 r_work: 0.3582 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26372 Z= 0.116 Angle : 0.596 19.499 36059 Z= 0.279 Chirality : 0.046 0.385 4304 Planarity : 0.004 0.053 4492 Dihedral : 7.769 75.436 5222 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.31 % Allowed : 12.97 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.15), residues: 3077 helix: 1.77 (0.21), residues: 655 sheet: 0.48 (0.19), residues: 728 loop : -1.30 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.024 0.001 TYR C 453 PHE 0.016 0.001 PHE B1121 TRP 0.007 0.001 TRP A 886 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00267 (26247) covalent geometry : angle 0.54626 (35724) SS BOND : bond 0.00277 ( 40) SS BOND : angle 1.30236 ( 80) hydrogen bonds : bond 0.04616 ( 972) hydrogen bonds : angle 4.56455 ( 2685) link_BETA1-4 : bond 0.00514 ( 35) link_BETA1-4 : angle 2.04191 ( 105) link_NAG-ASN : bond 0.00521 ( 50) link_NAG-ASN : angle 3.21865 ( 150) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 163 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.6564 (p90) cc_final: 0.5976 (p90) REVERT: A 153 MET cc_start: 0.4536 (pmm) cc_final: 0.3470 (tmm) REVERT: A 334 ASN cc_start: 0.9195 (t0) cc_final: 0.8584 (t0) REVERT: A 563 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.6329 (mp10) REVERT: A 663 ASP cc_start: 0.8361 (m-30) cc_final: 0.8149 (m-30) REVERT: A 754 LEU cc_start: 0.8279 (pp) cc_final: 0.8052 (mt) REVERT: A 878 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7718 (tt) REVERT: A 984 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8138 (pp) REVERT: A 1132 ILE cc_start: 0.8820 (pt) cc_final: 0.8585 (pt) REVERT: B 101 ILE cc_start: 0.8102 (mm) cc_final: 0.7738 (mp) REVERT: B 351 TYR cc_start: 0.7542 (p90) cc_final: 0.6965 (p90) REVERT: B 358 ILE cc_start: 0.7297 (mt) cc_final: 0.7087 (mm) REVERT: B 569 ILE cc_start: 0.4391 (OUTLIER) cc_final: 0.4123 (mp) REVERT: C 32 PHE cc_start: 0.7912 (m-10) cc_final: 0.7536 (m-80) REVERT: C 52 GLN cc_start: 0.7867 (tm-30) cc_final: 0.7624 (tm-30) REVERT: C 168 PHE cc_start: 0.8205 (t80) cc_final: 0.7999 (t80) REVERT: C 347 PHE cc_start: 0.8104 (m-10) cc_final: 0.7750 (m-10) REVERT: C 414 GLN cc_start: 0.7942 (mm-40) cc_final: 0.7536 (mt0) REVERT: C 523 THR cc_start: 0.8357 (p) cc_final: 0.7942 (t) REVERT: C 551 VAL cc_start: 0.7984 (OUTLIER) cc_final: 0.7765 (m) REVERT: C 564 GLN cc_start: 0.7575 (mm110) cc_final: 0.7316 (mm-40) REVERT: C 569 ILE cc_start: 0.5900 (OUTLIER) cc_final: 0.5480 (mp) REVERT: C 740 MET cc_start: 0.8516 (tpt) cc_final: 0.7997 (mtt) REVERT: C 814 LYS cc_start: 0.8945 (mmtt) cc_final: 0.8659 (mmmt) REVERT: C 918 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.7431 (mp0) REVERT: C 950 ASP cc_start: 0.8219 (t70) cc_final: 0.7917 (m-30) outliers start: 63 outliers final: 41 residues processed: 211 average time/residue: 0.1366 time to fit residues: 50.1399 Evaluate side-chains 206 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 158 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 164 optimal weight: 2.9990 chunk 214 optimal weight: 0.9990 chunk 149 optimal weight: 0.0970 chunk 118 optimal weight: 0.9980 chunk 202 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 198 optimal weight: 0.0980 chunk 184 optimal weight: 0.8980 chunk 286 optimal weight: 0.9980 chunk 213 optimal weight: 5.9990 chunk 182 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN B 774 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.196131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.148853 restraints weight = 32961.747| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 3.71 r_work: 0.3586 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26372 Z= 0.111 Angle : 0.586 19.524 36059 Z= 0.274 Chirality : 0.045 0.389 4304 Planarity : 0.004 0.053 4492 Dihedral : 7.340 71.720 5222 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.98 % Allowed : 13.26 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.15), residues: 3077 helix: 1.78 (0.21), residues: 660 sheet: 0.47 (0.19), residues: 728 loop : -1.28 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 357 TYR 0.025 0.001 TYR C 453 PHE 0.016 0.001 PHE B1121 TRP 0.007 0.001 TRP A 886 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00255 (26247) covalent geometry : angle 0.54259 (35724) SS BOND : bond 0.00262 ( 40) SS BOND : angle 1.26087 ( 80) hydrogen bonds : bond 0.04497 ( 972) hydrogen bonds : angle 4.52023 ( 2685) link_BETA1-4 : bond 0.00513 ( 35) link_BETA1-4 : angle 2.02879 ( 105) link_NAG-ASN : bond 0.00500 ( 50) link_NAG-ASN : angle 2.95181 ( 150) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 161 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4494 (pmm) cc_final: 0.3438 (tmm) REVERT: A 334 ASN cc_start: 0.9140 (t0) cc_final: 0.8544 (t0) REVERT: A 563 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.6343 (mp10) REVERT: A 663 ASP cc_start: 0.8337 (m-30) cc_final: 0.8119 (m-30) REVERT: A 754 LEU cc_start: 0.8277 (pp) cc_final: 0.8047 (mt) REVERT: A 878 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7755 (tt) REVERT: A 984 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8117 (pp) REVERT: A 996 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8452 (mp) REVERT: A 1132 ILE cc_start: 0.8843 (pt) cc_final: 0.8618 (pt) REVERT: B 101 ILE cc_start: 0.8127 (mm) cc_final: 0.7773 (mp) REVERT: B 351 TYR cc_start: 0.7539 (p90) cc_final: 0.6967 (p90) REVERT: B 569 ILE cc_start: 0.4390 (OUTLIER) cc_final: 0.4121 (mp) REVERT: B 988 GLU cc_start: 0.7937 (pm20) cc_final: 0.7385 (pm20) REVERT: C 32 PHE cc_start: 0.7917 (m-10) cc_final: 0.7501 (m-80) REVERT: C 52 GLN cc_start: 0.7859 (tm-30) cc_final: 0.7634 (tm-30) REVERT: C 168 PHE cc_start: 0.8174 (t80) cc_final: 0.7939 (t80) REVERT: C 347 PHE cc_start: 0.8080 (m-10) cc_final: 0.7712 (m-10) REVERT: C 414 GLN cc_start: 0.7955 (mm-40) cc_final: 0.7545 (mt0) REVERT: C 523 THR cc_start: 0.8315 (p) cc_final: 0.7901 (t) REVERT: C 551 VAL cc_start: 0.7957 (OUTLIER) cc_final: 0.7746 (m) REVERT: C 569 ILE cc_start: 0.5902 (OUTLIER) cc_final: 0.5477 (mp) REVERT: C 740 MET cc_start: 0.8517 (tpt) cc_final: 0.7991 (mtt) REVERT: C 814 LYS cc_start: 0.8953 (mmtt) cc_final: 0.8661 (mmmt) REVERT: C 918 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.7432 (mp0) REVERT: C 950 ASP cc_start: 0.8222 (t70) cc_final: 0.7915 (m-30) outliers start: 54 outliers final: 39 residues processed: 202 average time/residue: 0.1372 time to fit residues: 48.1975 Evaluate side-chains 205 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 158 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 270 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 239 optimal weight: 0.0870 chunk 279 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 304 optimal weight: 1.9990 chunk 309 optimal weight: 0.4980 chunk 199 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.195210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.147684 restraints weight = 33132.186| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 3.68 r_work: 0.3575 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26372 Z= 0.133 Angle : 0.602 19.541 36059 Z= 0.284 Chirality : 0.046 0.400 4304 Planarity : 0.004 0.053 4492 Dihedral : 7.137 67.909 5222 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.98 % Allowed : 13.26 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.15), residues: 3077 helix: 1.70 (0.21), residues: 659 sheet: 0.46 (0.19), residues: 726 loop : -1.29 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 357 TYR 0.025 0.001 TYR C 453 PHE 0.020 0.001 PHE A1121 TRP 0.008 0.001 TRP B 436 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00318 (26247) covalent geometry : angle 0.55947 (35724) SS BOND : bond 0.00301 ( 40) SS BOND : angle 1.43237 ( 80) hydrogen bonds : bond 0.04800 ( 972) hydrogen bonds : angle 4.57177 ( 2685) link_BETA1-4 : bond 0.00499 ( 35) link_BETA1-4 : angle 2.01978 ( 105) link_NAG-ASN : bond 0.00485 ( 50) link_NAG-ASN : angle 2.95499 ( 150) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 158 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4580 (pmm) cc_final: 0.3527 (tmm) REVERT: A 334 ASN cc_start: 0.9117 (t0) cc_final: 0.8594 (t0) REVERT: A 563 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.6345 (mp10) REVERT: A 663 ASP cc_start: 0.8341 (m-30) cc_final: 0.8099 (m-30) REVERT: A 754 LEU cc_start: 0.8289 (pp) cc_final: 0.7948 (mt) REVERT: A 878 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7679 (tt) REVERT: A 984 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8096 (pp) REVERT: A 996 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8494 (mp) REVERT: A 1132 ILE cc_start: 0.8905 (pt) cc_final: 0.8687 (pt) REVERT: B 101 ILE cc_start: 0.8119 (mm) cc_final: 0.7767 (mp) REVERT: B 351 TYR cc_start: 0.7556 (p90) cc_final: 0.6979 (p90) REVERT: B 396 TYR cc_start: 0.7486 (m-10) cc_final: 0.7201 (m-10) REVERT: B 569 ILE cc_start: 0.4402 (OUTLIER) cc_final: 0.4068 (mp) REVERT: C 168 PHE cc_start: 0.8193 (t80) cc_final: 0.7965 (t80) REVERT: C 347 PHE cc_start: 0.8080 (m-10) cc_final: 0.7691 (m-10) REVERT: C 414 GLN cc_start: 0.7952 (mm-40) cc_final: 0.7550 (mt0) REVERT: C 523 THR cc_start: 0.8320 (p) cc_final: 0.7914 (t) REVERT: C 551 VAL cc_start: 0.7972 (OUTLIER) cc_final: 0.7759 (m) REVERT: C 569 ILE cc_start: 0.5892 (OUTLIER) cc_final: 0.5468 (mp) REVERT: C 740 MET cc_start: 0.8559 (tpt) cc_final: 0.8029 (mtt) REVERT: C 814 LYS cc_start: 0.8941 (mmtt) cc_final: 0.8653 (mmmt) REVERT: C 918 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.7421 (mp0) REVERT: C 950 ASP cc_start: 0.8228 (t70) cc_final: 0.7934 (m-30) outliers start: 54 outliers final: 43 residues processed: 199 average time/residue: 0.1424 time to fit residues: 48.9504 Evaluate side-chains 208 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 157 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 50 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 273 optimal weight: 1.9990 chunk 266 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 191 optimal weight: 0.0170 overall best weight: 1.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN C 764 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.192215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.146180 restraints weight = 33080.797| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 4.55 r_work: 0.3504 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 26372 Z= 0.185 Angle : 0.643 19.576 36059 Z= 0.306 Chirality : 0.048 0.436 4304 Planarity : 0.004 0.052 4492 Dihedral : 7.097 61.887 5222 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.02 % Allowed : 13.45 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.15), residues: 3077 helix: 1.50 (0.21), residues: 659 sheet: 0.37 (0.19), residues: 727 loop : -1.34 (0.14), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1039 TYR 0.025 0.001 TYR C 453 PHE 0.027 0.002 PHE A1121 TRP 0.008 0.001 TRP B 436 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00461 (26247) covalent geometry : angle 0.60046 (35724) SS BOND : bond 0.00360 ( 40) SS BOND : angle 1.67088 ( 80) hydrogen bonds : bond 0.05609 ( 972) hydrogen bonds : angle 4.72447 ( 2685) link_BETA1-4 : bond 0.00506 ( 35) link_BETA1-4 : angle 2.01175 ( 105) link_NAG-ASN : bond 0.00467 ( 50) link_NAG-ASN : angle 3.04182 ( 150) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 158 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.6135 (p90) cc_final: 0.5558 (p90) REVERT: A 153 MET cc_start: 0.4616 (pmm) cc_final: 0.3528 (tmm) REVERT: A 334 ASN cc_start: 0.9126 (t0) cc_final: 0.8558 (t0) REVERT: A 529 LYS cc_start: 0.8551 (mmmt) cc_final: 0.7796 (mmtm) REVERT: A 563 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.6340 (mp10) REVERT: A 663 ASP cc_start: 0.8472 (m-30) cc_final: 0.8223 (m-30) REVERT: A 754 LEU cc_start: 0.8257 (pp) cc_final: 0.7903 (mt) REVERT: A 878 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7611 (tt) REVERT: A 984 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8070 (pp) REVERT: A 996 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8552 (mp) REVERT: A 1132 ILE cc_start: 0.9024 (pt) cc_final: 0.8791 (pt) REVERT: B 101 ILE cc_start: 0.8075 (mm) cc_final: 0.7716 (mp) REVERT: B 351 TYR cc_start: 0.7635 (p90) cc_final: 0.7102 (p90) REVERT: B 396 TYR cc_start: 0.7487 (m-10) cc_final: 0.7192 (m-10) REVERT: B 569 ILE cc_start: 0.4349 (OUTLIER) cc_final: 0.4000 (mp) REVERT: B 703 ASN cc_start: 0.8940 (OUTLIER) cc_final: 0.8508 (p0) REVERT: B 988 GLU cc_start: 0.7924 (pm20) cc_final: 0.7634 (pm20) REVERT: C 347 PHE cc_start: 0.8084 (m-10) cc_final: 0.7660 (m-10) REVERT: C 414 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7566 (mt0) REVERT: C 523 THR cc_start: 0.8407 (p) cc_final: 0.8000 (t) REVERT: C 551 VAL cc_start: 0.7885 (OUTLIER) cc_final: 0.7681 (m) REVERT: C 569 ILE cc_start: 0.5776 (OUTLIER) cc_final: 0.5370 (mp) REVERT: C 740 MET cc_start: 0.8701 (tpt) cc_final: 0.8025 (mtt) REVERT: C 814 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8657 (mmmt) REVERT: C 950 ASP cc_start: 0.8401 (t70) cc_final: 0.8021 (m-30) outliers start: 55 outliers final: 43 residues processed: 201 average time/residue: 0.1355 time to fit residues: 47.2931 Evaluate side-chains 207 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 156 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 102 optimal weight: 0.5980 chunk 222 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 251 optimal weight: 8.9990 chunk 246 optimal weight: 7.9990 chunk 182 optimal weight: 0.3980 chunk 199 optimal weight: 0.9990 chunk 229 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 286 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.194900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.146753 restraints weight = 32877.067| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 3.77 r_work: 0.3574 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26372 Z= 0.121 Angle : 0.602 19.448 36059 Z= 0.284 Chirality : 0.046 0.423 4304 Planarity : 0.004 0.053 4492 Dihedral : 6.873 57.689 5222 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.98 % Allowed : 13.70 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.15), residues: 3077 helix: 1.67 (0.21), residues: 653 sheet: 0.42 (0.19), residues: 728 loop : -1.29 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 357 TYR 0.026 0.001 TYR C 453 PHE 0.016 0.001 PHE B1121 TRP 0.007 0.001 TRP A 886 HIS 0.003 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00280 (26247) covalent geometry : angle 0.55844 (35724) SS BOND : bond 0.00302 ( 40) SS BOND : angle 1.42649 ( 80) hydrogen bonds : bond 0.04835 ( 972) hydrogen bonds : angle 4.59002 ( 2685) link_BETA1-4 : bond 0.00522 ( 35) link_BETA1-4 : angle 2.04863 ( 105) link_NAG-ASN : bond 0.00509 ( 50) link_NAG-ASN : angle 2.96669 ( 150) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5683.04 seconds wall clock time: 98 minutes 6.16 seconds (5886.16 seconds total)